Yikes. Thanks James. Silly me - I've been running mpileup for a long time but always just piped it into something else (bcftools, etc.).
I think all the [$^] etc. are in the earlier versions so there appears to be a good chance the output is identical. thanks, Richard On 12/11/2015 01:57 AM, James Bonfield wrote: > Hi, > > On Thu, Dec 10, 2015 at 10:01:47AM -0800, Richard Corbett wrote: >> Hi all, >> We have some old legacy scripts that rely on the old pileup format: >> ... >> 1 180934047 T 5 cccCc @JG>F >> 1 180934163 A 5 gGgGG GHJFF >> 1 180938117 G 4 .,.. JBJA >> ... > How does that differ to the current output from mpileup? > > $ samtools mpileup -f hs37d5.fa 9827_2#49.bam > ... > 1 42744 C 2 ,, DE > 1 42745 A 2 ,, DD > 1 42746 C 3 ,,^!. CE; > 1 42747 A 3 ,,. CIC > 1 42748 A 3 ,,. BHB > 1 42749 T 3 ,,+1a. CCD > 1 42750 A 2 ,$. <E > 1 42751 A 1 . E > 1 42752 A 1 . D > > This has the addition of ^ and $ markers for read start/finish, along > with various indel marks too, but I thought they were in the old > pileup format too. (If not then it's a trivial sed statment to remove > these.) > > James -- The contents of this electronic mail transmission are intended to be CONFIDENTIAL and for the sole use of the designated recipient. If this message has been misdirected, please contact the sender as soon as possible. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
